Multiple platform build/check report for BioC 3.20 - BUILD BIN results for seqTools on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD BIN results for seqTools on palomino8

To the developers/maintainers of the seqTools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqTools.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: seqTools

Version: 1.40.0

Command: rm -rf seqTools.buildbin-libdir && mkdir seqTools.buildbin-libdir && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=seqTools.buildbin-libdir seqTools_1.40.0.tar.gz

StartedAt: 2024-11-18 08:39:16 -0500 (Mon, 18 Nov 2024)

EndedAt: 2024-11-18 08:40:20 -0500 (Mon, 18 Nov 2024)

EllapsedTime: 63.6 seconds

RetCode: 0

Status: OK

PackageFile: seqTools_1.40.0.zip

PackageFileSize: 654.4 KiB

Command output

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###
### Running command:
###
###   rm -rf seqTools.buildbin-libdir && mkdir seqTools.buildbin-libdir && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=seqTools.buildbin-libdir seqTools_1.40.0.tar.gz
###
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* installing *source* package 'seqTools' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c seqTools.c -o seqTools.o
seqTools.c: In function 'count_genome_Kmers':
seqTools.c:851:93: warning: format '%u' expects a matching 'unsigned int' argument [-Wformat=]
  851 |                                 error("[count_genome_Kmers] character mismatch at position %u!");
      |                                                                                            ~^
      |                                                                                             |
      |                                                                                             unsigned int
seqTools.c: In function 'scale_kmer_matrix':
seqTools.c:3296:55: warning: format '%i' expects argument of type 'int', but argument 3 has type 'double' [-Wformat=]
 3296 |                 error("[scale_kmer_matrix] scale[%i]=%i must be >1!", column_index, scale);
      |                                                      ~^                             ~~~~~
      |                                                       |                             |
      |                                                       int                           double
      |                                                      %f
seqTools.c:3306:73: warning: format '%i' expects argument of type 'int', but argument 3 has type 'double' [-Wformat=]
 3306 |                                 error("[scale_kmer_matrix] scale[%i] = %i must be >1!", column_index, scale);
      |                                                                        ~^                             ~~~~~
      |                                                                         |                             |
      |                                                                         int                           double
      |                                                                        %f
gcc -shared -s -static-libgcc -o seqTools.dll tmp.def seqTools.o -lm -LF:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/meat/seqTools.buildbin-libdir/00LOCK-seqTools/00new/seqTools/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
In fun(libname, pkgname) :
  Package 'zlibbioc' is deprecated and will be removed from Bioconductor
  version 3.22
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'zlibbioc' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'zlibbioc' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'seqTools' as seqTools_1.40.0.zip
* DONE (seqTools)